GitTyee
Eric
2023-07-12
1. What is this?
A high-level, and very casual, look at trends in catches of Tyee salmon in Campbell River’s legendary Tyee Pool. All data exploration is being completed for fun and to learn some new tools (namely R Markdown and plotly).
There are far more technical ways of examining this data, but they aren’t as much fun - and are frankly hard. This analysis is living and will evolve over time. All results and interpretation are purely speculative and should be considered nothing more than ramblings of a fish nerd.
1.1 The data
This analysis uses the following publicly available data:
- Annual catch records from the Tyee Club.
- Discharge data collected on the Campbell River by the Water Survey of Canada.
- Annual Chinook Salmon escapement data available in the DFO NuSEDS database.
- Annual catch statistics from the North Pacific Anadromous Fish Commission
- Area based commercial catch statistics from DFO are available from 2001 to 2016
This is certainly an interesting dataset, especially given it is the Tyee Club centenary, but it has its limitations. For example, there is no information on effort (# boats per day) and biological data is limited (e.g. size, girth and age of tyees or number of undersized fish captured).
2. Chinook Salmon
2.1 What we* know about Campbell River Chinook?
(* more like, what do I know, which isn’t much).
There has been a lot of information collected on Campbell River Chinook Salmon, including from Tyee Salmon captured in the Tyee Pool, however, most of this data is not readily available online. Data that is available (and that I have found) is summarized below.
2.1.1 Spawn Timing
- Chinook spawning occurs from late September through early November and peaks in mid-October and that spawners reside in the river for ~12 days.
2.1.2 Age Class Structure
A roughly equal proportion of spawners return to the Campbell River as age-4 and age-5 fish (see Table 1) Sturham et al. 1999.
However, Ewart & Anderson,2013 report that Age-5 fish were dominant in 2012 (61%), with Age-4’s accounting for only 37% of the run, and age-3’s representing only 2%.
2.1.3 Size-at-Age
- I have not found any measures of individual fish. But binned data from Sturham et al. 1999 shows that Age-4 fish generally range in size from 550-949 mm (mean ~ 780 mm) and age-5 fish range from 700-949 mm (mean ~ 840 mm). Age-6 fish were identified, but accounted for less than 1% of all fish in the Campbell (n = 1 fish, 930 mm) and Quinsam rivers
2.1.4 Fecundity
- Ewart & Anderson, 2013 report that female Chinook in the Campbell River in 2012 carried roughly ~5,700, a decrease from the roughly 6,000 eggs typically carried.
2.1.5 Juvenile Life History
- Juvenile Chinook Salmon in the Campbell River have been studied intensively since 2015 (e.g. Thornton et al. 2022. These data suggests fry emerge in February-March and that nearly all Campbell River Chinook out migrate as Age-0+ juveniles from March through July. Smaller recently emerged Age-0+ fry are dominant and typically captured from March through early May (37 to 52 m). Larger Age-0+ smolts are less common and move out from May through July (64 to 88 mm).
2.1.6 Estimated Juvenile Production
- Estimates of juvenile Chinook production based on numbers of observed spawners have generally been less than numbers trapped throughout the outmigration period (Thornton et al. 2022, which may be due to increased juvenile survival or inaccurate/coarse estimates of fecundity.
2.1.7 Estimates of Marine Survival
- Marine survival of unfed fry released from the Quinsam hatchery range from 0.2% to 0.4% (yes, that is less than 1%) (Ewart & Anderson 2013).
2.1.8 Hatchery Influence and Population Status
- Ewart & Anderson 2013 report that 56% of the otoliths examined from the 2012 return showed no signs of hatchery marking and are assumed wild. The remaining 44% are presumed to have originated from instream incubators (31%), seapen released smolts (4%) and Quinsam River released smolts (9%).
| Waterbody | Age | n | % of Total | Size Range (mm) |
Mean Lenght (mm) |
|---|---|---|---|---|---|
| Campbell River | 3 | 6 | 7.9 | 500 - 699 | 595.0 |
| Campbell River | 4 | 34 | 44.7 | 550 - 949 | 779.5 |
| Campbell River | 5 | 35 | 46.1 | 700 - 949 | 842.5 |
| Campbell River | 6 | 1 | 1.3 | 900 - 949 | 930.0 |
| Quinsam Hatchery | 3 | 76 | 20.2 | 400 - 749 | 619.5 |
| Quinsam Hatchery | 4 | 225 | 59.8 | 550 - 899 | 743.5 |
| Quinsam Hatchery | 5 | 73 | 19.4 | 700 - 949 | 834.0 |
| Quinsam Hatchery | 6 | 2 | 0.5 | 750 - 849 | 784.0 |
| Quinsam River | 3 | 46 | 22.8 | 500 - 849 | 663.0 |
| Quinsam River | 4 | 114 | 56.4 | 550 - 949 | 733.5 |
| Quinsam River | 5 | 40 | 19.8 | 700 - 949 | 818.0 |
| Quinsam River | 6 | 2 | 1.0 | 800 - 849 | 838.0 |
2.2 What else do we know about current Chinook Salmon trends?
2.2.1 They are decreasing in size and age at maturity
- Ohlberger et al. 2018 have shown that there is a reduction in the proportion of older age classes throughout most regions of the East Pacific and that length-at-age of older fish has decreased while length-at-age of smaller fish has increased.
- Malick
et al. 2023 compiled 3 decades worth of broodstock data from 43
hatcheries to examine trends in fecundity. They found significant
changes in both fecundity and length, with the greatest drop in
fecundity occurring over the past decade. Interestingly, they also
estimate that a 1 mm reduction in length results in ~7.8 few eggs per
female.
- Oke et al. 2020 state that relative to salmon maturing before 1990, adult Chinook salmon now produce 16% fewer eggs, transport 28% less nutrients and have lost 21% of their fisheries value.
2.2.2 Survival rates have collapsed and returns are decreasing
Welch et al. 2018 used coded-wire tag data to look at large scale patterns of Chinook salmon survival. This data demonstrates that survival collapsed over the past half century by a factor of ~3 and is currently ~1% in many regions (consistent with estimates available for the Campbell). Survival in relatively pristine and undeveloped regions (e.g. Northern BC and Alaska) was comparable to areas with extensive water management and land development that were previously considered to have poorest survival (e.g. Columbia River). The authors suggest the widespread trends in survival may be evidence that marine conditions are more influential than local factors (e.g. freshwater habitat).
Similar trends have been observed in other species. For example, Price et al. 2021 found a 69% reduction in wild Sockeye salmon returns (though overall returns are comparable to historic levels due to intensive enhancement); that population diversity has decreased by ~70%, and; that life history diversity has shifted with populations now migrating from freshwater earlier and remaining at sea for longer.
2.2.3 Enhancement levels have never been higher
- Ruggerone
& Irvine 2018 show that intensive enhancement has resulted in
the greatest abundance of salmon in the ocean than ever before
(specifically pink, sockeye and chum) and that marine carrying capacity
may have been reached within recent decades.
- Nelson et al. 2019 present evidence that hatchery practices have altered size and time that juveniles are released and have reduced diversity of life history traits (e.g. size, age and timing of smoltification). The authors argue that current enhancement practices may release fish at a time and size that is preferred by predators (e.g. all fish being released at same time and size and are easy pickings for large aggregations of predators).
2.2.4 I am not the only person who doesn’t understand what is going on
- Beamish 2022 emphasizes that due to the large number of juvenile salmon in the ocean and overall poor survival, any small change in survival can results in major changes in adult abundance. Unfortunately, we don’t understand what is causing those small changes in survival in the marine environment and need a better understanding of biologically based mechanisms linking climate change to salmon abundance.
3. Let’s look at the Tyee catch data!
So, let’s begin by having a look at the catch data from the Tyee pool and how catches fluctuate relative to Chinook Salmon escapement in the Campbell River.
Figure 1: Trends in Tyee Salmon captures and Campbell River Chinook Salmon escapement.
A quick look at Tyee catches (blue vertical bars) in Figure 1 shows:
- There is a fairly clear 4-year cycle of relatively higher catches (highlighted with shading). Which is interesting, and raises lots of questions…
- There has been a consistent decline in the number of Tyee salmon captured per year.
- There was a major crash or failure in 2014.
If we look at Escapement data (blue line) shown in Figure 1 , we can see:
- There has been a general declining trend in escapement (consistent with regional trends),
- Periods of increased escapement correspond with periods of increased Tyee catches, but not always (e.g. 2005, 2017 and 2020). Given the lack of information on effort (e.g. # of boats fishing per day) we cannot tease apart whether the lack of catches in some years is due to reduction in pressure.
- It is also possible that years with high escapement and low Tyee numbers were due to an increased proportion of smaller fish returning to the Campbell. Without annual information on age structure I cannot tease this apart.
3.1. What could be affecting returns and catches?
At it’s most basic level, there are four things that are likely affecting catches of Tyee salmon (in reality, there are many many many many many more.
3.1.1. Juvenile recruitment
- This is determined by the number of eggs that are deposited (for easy math, lets say females account for 50% of escapement, that each one deposits 4000 eggs and that egg to fry survival is 10%). We will assume that fish that survive to fry will enter the sea. Hydrometric data on the Campbell is available back to 1949 and it is likely that extreme high or low flow events (e.g. greater than 300 cms, less than ??50 cms??) during the incubation/rearing periods (maybe November through March) will reduce juvenile recruitment.
3.1.2. Marine survival and productivity
- This is way too complicated for right now. Let’s feel warm and fuzzy by assuming survival and productivity are stable (side note, they arent!). But if we don’t do this we can’t assume that proportions calculated from Sturham et al. are representative of current returns (unfortunately recent evidence shows this assumption is wrong and that fish are decreasing in size, so there are likely fewer Tyee returning now than in previous years).
3.1.3. Fishing effort and catchability
- For now, I am going to assume effort (# of boats fishing per tide/day) is constant and that catchability (percent of Tyees present that are captured) are stable. In reality, effort has likely decreased over time (especially since 2014) and catchability has likely increased as peoples knowledge, skill and fishing technology have improved over time (not everyone though, I still suck). Either way, without some hard data it is hard to much with this.
3.1.4. Fishing Conditions
- No question that fewer fish will be captured during seasons with poor fishing conditions (e.g. very windy, lots of rain). It is also possible that fish behaviour will change in response to river conditions. Certainly there was a lot of speculation that high flows during the 2022 Tyee season contributed to record low catches.
4. So, what can we look at?
Off the top of my head there are two ways we can approach this:
1.) We can look at what factors influenced how many fish were available for capture in the Tyee pool (i.e. how historic conditions may have contributed to observed captures), and/or; 2.) We can look at what factors influenced how returning fish were captured (i.e. conditions during the fishing season)
4.1 How Historic Conditions Influenced Captures
We can VERY CRUDELY estimate the number of Tyee salmon that should return to the Campbell River if we make a couple of big assumptions:
Fecundity is ~5,700 eggs per female (Ewart & Anderson, 2013
Sex ratios are 60:40 female to male (Sturham et al. 1999. on Sturham data for Campbell River)
Egg to fry survival is approximately 0.003 (estimated from Thronton et al. 2022).
Tyee Salmon are over 900 mm. In the Campbell River, I will assume that 10% of Age-4 male adults, 15% of Age-5 spawners (both sexes), and all Age-6 fish are >900 mm and therefore >30 lbs (this is very loosely based on Sturham data, but I have not seen raw tables so its an guestimate).
Using these numbers we can assume that 60% of a given years fish will be female and spawn successfully. Each one will lay ~5,700 eggs, of which 0.3% will survive to spawn. Of the 0.3% of eggs that survive to spawn, 44.7% will return as Age-4 (15% will be Tyees), 46.1% will return as Age-5 (35% will be Tyees) and 1.3% will return as Age-6 fish (85% will be Tyees).
If we run these numbers, each female will generate 17.1 offspring, of which 7.6 will be Age-4, 7.9 will be Age-5 and 0.22 will be Age-6 - of which 3.4 will be Tyee salmon.
But this doesn’t make sense, if each female produced 17.1 offspring escapement would be increasing rapidly. And it most certainly is not. So, what gives?
Figure 2: Comparison of catches of Tyee Salmon, predicted returns of Tyee Salmon and annual Chinook Salmon escapement counts.
Well, even though my estimates are clearly wrong, this is still interesting. There is a fairly drastic shift in predicted returns that coincides with the crash in 2014. Prior to the crash, predicted returns are consistently underestimated (73% of years are less than actual catches) whereas after the crash predicted Tyee returns are greater than total tyee catches in all but one year. Not sure exactly what this means, or how to interpret it, but I think its worth considering:
- Only a proportion of all returning Tyees are captured each year. If
all Tyee salmon were captured each year, we would be actively selecting
against large fish and it would be reasonable to expect to see a
continuous decline in the total number of Tyees returning each year. So,
based on this logic (and my personal observation of tyees on the
spawning ground), the predicted Tyee returns should always be greater
than total catches.
- The formula and values used to estimate predicted returns of tyee salmon do not change. If we assume there is no change in catchability and that the number of Tyees captured in the pool is a representation of the actual number of Tyee salmon that return to the river there appears to have been a dramatic reduction in the number or proportion of Tyee salmon in 2014. Given low escapement in 2014, it is most likely a poor return rather than a reduced proportion of Tyee.
- Additionally, the figure shows that my formula and estimates are way off - which is not surprising as they were very crude! This is most apparent in the years prior to the 2014 crash, but suggests predictions after the crash are also off too.
So, what happened in 2014!? Did runs crash everywhere? Let’s have a look at escapement in other systems in the area.
Figure 3: Chinook Salmon escapement from rivers on East and West Coast of Vancouver Island.
Well, that figure sucks. But it shows how variable escapement is between years. On the East Coast of the Island, abundance increased in ’r format(3/7*100, digits = 2)`% of plotted streams and decreased in all others. Decreases
Relative to 2013, abundance in all plotted west coast streams was slightly reduced in 2014. There was a major crash in the Burnam River, but this is exaggerated by unusually high returns in 2013, 2015 and 2016.
MAYBE RERUN ESCAPEMENT PLOT USING ALL ESCPAEMENT DATA!? FACET BY AREA?
ADD METRIC THAT STANDARDIZES ESCAPEMENT. E.G. total annual returns vs mean annual returns.
Influence of river flow on catches
Last year there was a lot of speculation that high flows in the Campbell River may have caused fish to move directly into the river rather than staging in the pool. Let’s look at flow in the Campbell River to see how 2022 flows compared to previous years.
Figure 4: Catches of Tyee Salmon since 2016 relative to flow in the Campebll River.
Well, it’s clear that flows in 2022 were higher than past years and higher than mean flows over the past 5-years. But this doesn’t mean that is why fewer fish were captured. Either way let’s take a closer look at the correlation between flow and capture.
## `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
Figure 5: Relationship between river flow and fish capture
Figure 5 shows a strong negative relationship between discharge and the number of fish that are captured. This is what you would expect, that fish will hold in the pool while flows are low and that they will move into the river when flows are higher and they can safely navigate upstream. However, the fishery occurs during the late summer, when flows are typically low and it is possible that the timing of the fishery has contributed to observed trends.
OK, well there is a relationship (that could be due to a number of things). Lets have a look at some of the older data.
Figure 6: Catches of Tyee Salmon since 2007 relative to flow in the Campebll River.
Let’s look at commercial catches. Maybe there is a fishery that could be intercepting a large number of Tyees.
can.catch <- comm.catch %>% rename(Catch.Type = 'Catch Type',
Data.Type = 'Data Type') %>%
mutate(Area = as.factor(Area),
Species = as.factor(Species),
Year = as.numeric(Year),
Catch.Type = as.factor(Catch.Type)) %>%
filter(Country == "Canada",
Year >= 1997,
Data.Type == "Number (000's)")
can.catch.cn <- can.catch %>% filter(Species == "Chinook",
Area == "Whole country")
CN.catch.plot <- ggplot(can.catch.cn) +
geom_line(aes(x = Year, y = Total.Catch, color = Catch.Type)) +
labs(x = "Year", y = "Total Catch (0000's of fish") +
theme_bw()
CN.catch.plot
can.catch.cn2 <- can.catch %>% filter(Species == "Chinook",
Catch.Type == "Sport")
summary(can.catch.cn2)## Country Whole Country/Province/State
## Length:125 Length:125
## Class :character Class :character
## Mode :character Mode :character
##
##
##
##
## Area Species Catch.Type
## Haida Gwaii :25 Chinook:125 Commercial : 0
## North Coast :25 Cherry : 0 Sport :125
## South Coast :25 Chum : 0 Subsistence: 0
## West Coast Vancouver Island:25 Coho : 0
## Whole country :25 Pink : 0
## Amur River Basin : 0 Sockeye: 0
## (Other) : 0 (Other): 0
## Data.Type Year Total.Catch
## Length:125 Min. :1997 Min. : 0.00
## Class :character 1st Qu.:2003 1st Qu.: 25.80
## Mode :character Median :2009 Median : 54.00
## Mean :2009 Mean : 77.34
## 3rd Qu.:2015 3rd Qu.: 92.49
## Max. :2021 Max. :306.68
## CN.catch.plot2 <- ggplot(can.catch.cn2) +
geom_line(aes(x = Year, y = Total.Catch, color = Area)) +
labs(x = "Year", y = "Total Catch (0000's of fish") +
theme_bw()
CN.catch.plot2
can.catch.sk <- can.catch %>% filter(Species == "Sockeye")
colnames## function (x, do.NULL = TRUE, prefix = "col")
## {
## if (is.data.frame(x) && do.NULL)
## return(names(x))
## dn <- dimnames(x)
## if (!is.null(dn[[2L]]))
## dn[[2L]]
## else {
## nc <- NCOL(x)
## if (do.NULL)
## NULL
## else if (nc > 0L)
## paste0(prefix, seq_len(nc))
## else character()
## }
## }
## <bytecode: 0x000001c3318b15c0>
## <environment: namespace:base>summary(can.catch.cn2)## Country Whole Country/Province/State
## Length:125 Length:125
## Class :character Class :character
## Mode :character Mode :character
##
##
##
##
## Area Species Catch.Type
## Haida Gwaii :25 Chinook:125 Commercial : 0
## North Coast :25 Cherry : 0 Sport :125
## South Coast :25 Chum : 0 Subsistence: 0
## West Coast Vancouver Island:25 Coho : 0
## Whole country :25 Pink : 0
## Amur River Basin : 0 Sockeye: 0
## (Other) : 0 (Other): 0
## Data.Type Year Total.Catch
## Length:125 Min. :1997 Min. : 0.00
## Class :character 1st Qu.:2003 1st Qu.: 25.80
## Mode :character Median :2009 Median : 54.00
## Mean :2009 Mean : 77.34
## 3rd Qu.:2015 3rd Qu.: 92.49
## Max. :2021 Max. :306.68
## CN.catch.plot
sk.catch.plot <- ggplot(can.catch.sk) +
geom_line(aes(x = Year, y = Total.Catch, color = Species, linetype = Catch.Type))
sk.catch.plot
###Notes Plot peak flows 4 to 5 years previous (e.g. impact of peak flows on recruitment). - Assume mortality at >200 cms - spawning habitat lost at 300-400 cms - Is Quinsam flow regulated? Ask Mary.
Is return age genetic? Or environmental?
Supplemental Tables and Figures
| Waterbody | Sex | Age | n | % of Total (by Sex) |
% of Total (by Stream) |
Size Range (mm) |
Mean Lenght (mm) |
Std. Error |
|---|---|---|---|---|---|---|---|---|
| Campbell River | F | 3 | 0 | 0.00 | 0.00 | 500 - 699 | 595 | 20.82 |
| Campbell River | M | 3 | 6 | 0.19 | 0.08 | 500 - 699 | 595 | 20.82 |
| Campbell River | F | 4 | 21 | 0.48 | 0.28 | 700 - 899 | 783 | 10.69 |
| Campbell River | M | 4 | 13 | 0.41 | 0.17 | 550 - 949 | 776 | 23.30 |
| Campbell River | F | 5 | 23 | 0.52 | 0.30 | 750 - 949 | 839 | 7.51 |
| Campbell River | M | 5 | 12 | 0.38 | 0.16 | 700 - 949 | 846 | 14.43 |
| Campbell River | F | 6 | 0 | 0.00 | 0.00 | 900 - 949 | 930 | 0.00 |
| Campbell River | M | 6 | 1 | 0.03 | 0.01 | 900 - 949 | 930 | 0.00 |
| Quinsam Hatchery | F | 3 | 9 | 0.04 | 0.02 | 550 - 749 | 644 | 15.33 |
| Quinsam Hatchery | M | 3 | 67 | 0.38 | 0.18 | 400 - 749 | 595 | 6.84 |
| Quinsam Hatchery | F | 4 | 130 | 0.65 | 0.35 | 600 - 899 | 742 | 3.77 |
| Quinsam Hatchery | M | 4 | 95 | 0.54 | 0.25 | 550 - 899 | 745 | 5.64 |
| Quinsam Hatchery | F | 5 | 61 | 0.30 | 0.16 | 700 - 949 | 823 | 5.76 |
| Quinsam Hatchery | M | 5 | 12 | 0.07 | 0.03 | 750 - 949 | 845 | 13.57 |
| Quinsam Hatchery | F | 6 | 1 | 0.00 | 0.00 | 800 - 849 | 812 | 0.00 |
| Quinsam Hatchery | M | 6 | 1 | 0.01 | 0.00 | 750 - 799 | 756 | 0.00 |
| Quinsam River | F | 3 | 1 | 0.01 | 0.00 | 700 - 749 | 700 | 0.00 |
| Quinsam River | M | 3 | 45 | 0.41 | 0.22 | 500 - 849 | 626 | 12.07 |
| Quinsam River | F | 4 | 58 | 0.63 | 0.29 | 650 - 849 | 744 | 4.73 |
| Quinsam River | M | 4 | 56 | 0.51 | 0.28 | 550 - 949 | 723 | 9.35 |
| Quinsam River | F | 5 | 31 | 0.34 | 0.15 | 700 - 949 | 830 | 7.54 |
| Quinsam River | M | 5 | 9 | 0.08 | 0.04 | 700 - 949 | 806 | 21.00 |
| Quinsam River | F | 6 | 2 | 0.02 | 0.01 | 800 - 849 | 838 | 2.83 |
| Quinsam River | M | 6 | 0 | 0.00 | 0.00 | 800 - 849 | 838 | 2.83 |